NAMD: A parallel, object-oriented molecular dynamics program

Mark T. Nelson; William Humphrey; Attila Gursoy; Andrew Dalke; Laxmikant V. Kale; Robert D. Skeel; Klaus Schulten

doi:10.1177/109434209601000401

NAMD: A parallel, object-oriented molecular dynamics program

Mark T. Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant V. Kale, Robert D. Skeel, Klaus Schulten

Research output: Contribution to journal › Article › peer-review

Abstract

NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design implemented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decomposition coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed parallel multipole tree algorithm for full electrostatic force evaluation in O(N) time. NAMD can be connected via a communication system to a molecular graphics program in order to provide an interactive modeling tool for viewing and modifying a running simulation. The application of NAMD to a protein-water system of 32,867 atoms illustrates the performance of NAMD.

Original language	English (US)
Pages (from-to)	251-268
Number of pages	18
Journal	International Journal of High Performance Computing Applications
Volume	10
Issue number	4
DOIs	https://doi.org/10.1177/109434209601000401
State	Published - 1996

ASJC Scopus subject areas

Software
Theoretical Computer Science
Hardware and Architecture

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AU - Kale, Laxmikant V.

AU - Skeel, Robert D.

AU - Schulten, Klaus

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NAMD: A parallel, object-oriented molecular dynamics program

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